Datasets:
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Long-term data that utilise standardised and structured methodologies are ideal for quantifying change in bird populations. With increasing interest in quantifying the drivers of biodiversity responses to climate change and other forms of environmental change, the perspective that comparisons with older datasets provid... |
Tombusvirus-like associated RNAs (tlaRNAs) are autonomously replicating + ssRNAs of about 2.8 kb that are most closely related to viruses of the family *Tombusviridae*. Encoding only an RNA dependent RNA polymerase (RdRp) which enables their independent replication, tlaRNAs rely on one or more co-infecting viruses, typ... |
Biobased and biodegradable polyhydroxyalkanoates (PHAs) have attracted a recent interest in the scientific community based on their properties, which are very similar to those of conventional plastics such as polypropylene or polystyrene. To date, more than 55 species of Gram-positive and Gram-negative bacteria have be... |
The clinical picture of pulmonary artery embolism secondary to deep vein thrombosis falls under the term venous thromboembolism (VTE). VTE is a common cardiovascular event with increasing incidence. The fact that acute pulmonary artery embolisms (PE) may be asymptomatic or show only non-specific symptoms is a challenge... |
Breast cancer (BC) is currently recognized as one of the most commonly diagnosed malignancies in the worldwide, and it is the fifth leading cause of cancer-related deaths. According to data from GLOBOCAN 2020, approximately 2.3 million new cases of breast cancer are expected to be diagnosed worldwide. In addition to it... |
1. Introduction
Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) in the last two decades has been largely applied to the qualitative and quantitative analysis of low molecular weight compounds (LMWC). However, some major drawbacks persist as (i) the variability of signal intensities and resolu... |
The binding of a transcription factor to a regulatory region (*e.g*., gene promoter) perturbs the expression of the gene. ChIP experiments identify potential binding sites. However, these experiments produce hundreds or thousands of peaks for most factors. Therefore, methods that determine which of these binding sites ... |
Eukaryotic gene expression relies on accurate and timely splicing of pre-mRNA transcripts by the spliceosome. The spliceosome is an RNA-protein complex that assembles anew on each intron and proceeds through a litany of compositional and conformational changes as it executes the reactions necessary to remove the intron... |
There is a sudden reawakening of interest in using subanaesthetic concentrations of N~2~O in psychiatry. Thus, we need answers to these questions. Particularly, as research has already shown the greater safety and wider usefulness of correctly titrated subanaesthetic N~2~O for psychiatry.
The technique recently advocat... |
Anisakiasis is a parasitic disease in humans caused by the incidental ingestion of *Anisakis* larvae, which are present in fresh fish and squid. When the larvae stick to the gastrointestinal membrane and cause various kinds of symptoms, the status is termed as anisakiasis. According to the location where the *Anisakis*... |
Eukaryotic genomics has overwhelmingly focused on multicellular organisms, in spite of the staggering diversity of unicellular eukaryotes. When unicellular eukaryotes are studied, it is still mostly in connection to human health or economic interests. One of the most prominent examples of this limited and biased sampli... |
Of the 625,000 and 619,000 deaths caused by malaria in 2020 and 2021, respectively, 76% were children under 5 years old, primarily in sub-Saharan Africa. The 2020 peak represents 57,000 more deaths than in 2019, a 10% increase in mortality that has been attributed to disruptions due to the COVID-19 pandemic. Malaria is... |
1. Introduction
Breast cancer-related lymphedema is a common complication following breast cancer treatment, which severely affects patients' quality of life. The treatment of lymphedema has always been difficult. This may be because, when most patients are diagnosed with lymphedema, the lymphedema is already serious, ... |
During volitional object manipulation, haptic sensations (proprioceptive, kinesthetic, and tactile) from the biological limb are used to make grasp corrections and update internal feedforward models of the object and environment. This model refinement helps improve the speed and dexterity of subsequent manipulations, s... |
1 Introduction
Chemical neurotransmission is terminated by two fundamentally distinct mechanisms that remove active neurotransmitters from the extracellular space: enzymatic extracellular degradation and transmembrane cellular uptake, respectively. Drugs that target either of these two diverging mechanisms exert pronou... |
All relevant data files are publicly available from the National Agriculture Library "Ag Data Commons" database.
The true fruit flies (Diptera: Tephritidae) comprise over 4,000 species, approximately 250 of which are serious agricultural pests of fleshy fruits and vegetables Established tephritid pests are commonly con... |
In German mythology, there is a story of a water nymph named Ondine, who falls in love with a mortal. When she discovers that he has been unfaithful to her, she curses him to stop breathing should he ever go to sleep. The myth of "Ondine's curse" has made its way into modern medicine by way of a disorder called congeni... |
1. Introduction
Adipose-derived stem cells (ADSCs) are mesenchymal stem cells that are known for their angiogenic properties, plasticity, and multipotent ability to differentiate into different cell lineages, such as chondrogenic, adipogenic, and osteogenic. Mesenchymal stem cells can be obtained from various sites, su... |
1. Introduction
The epithelial--mesenchymal transition (EMT) stands out as one of the main molecular processes that drive cancer progression by facilitating cell migration, metabolic reprogramming, and interactions between the tumor and immune system. EMT has been traditionally regarded as a binary transition between a... |
To the editor
Acute myeloid leukemia (AML) mostly occurs in middle-aged and elderly patients, and coronary heart disease (CHD) is one of the most common concomitant diseases in this population. AML patients with severe CHD are extremely challenging for clinicians, moreover, there is no clinical experience to follow for... |
There is a global trend of increased usage of health questionnaires (scales), both in population health surveys and in health care systems, as patient-reported measures. In multipurpose surveys with a need to use several scales on different issues, such as psychosocial factors and health status, these surveys tend to b... |
Ovarian cancer is the most lethal of all gynecologic malignancies. Surgery with complete residual tumor removal (R0 resection) is the recommended treatment and has the greatest prognostic impact. To obtain complete cytoreduction, patients with advanced ovarian cancer often undergo en bloc rectosigmoid resection with to... |
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PMC 1024-2040 Biomedical Fine-Tuning Corpus
Summary
This is a cleaned biomedical long-text corpus for autoregressive language-model fine-tuning and held-out evaluation.
| split | rows | role |
|---|---|---|
| train | 10,000 | fine-tuning |
| test | 1,000 | held-out evaluation |
The public schema is text-only:
text: string
No PMCID, date, license, URL, or provenance fields are included in the public dataset files.
Token Contract
The corpus is built for EleutherAI/pythia-2.8b.
Token counts were computed with:
tokenizer.encode(text, add_special_tokens=False)
| requirement | value |
|---|---|
| stored text minimum | 1024 tokens |
| stored text maximum | 2039 tokens |
| EOS token budget | +1 token |
| maximum sequence budget | 2040 tokens |
| EOS stored inside text | no |
Final token-count statistics:
| stat | train | test |
|---|---|---|
| min | 1025 | 1048 |
| mean | 1953.9 | 1950.8 |
| median | 2002 | 2000 |
| max | 2039 | 2039 |
| p1 | 1228.0 | 1185.8 |
| p5 | 1640.0 | 1644.0 |
| p25 | 1966.0 | 1960.0 |
| p75 | 2021.0 | 2021.0 |
| p95 | 2035.0 | 2034.0 |
| p99 | 2039.0 | 2039.0 |
Source
Source dataset:
common-pile/pubmed_filtered
Rows were filtered to:
| filter | requirement |
|---|---|
| publication date | publication_date >= 2020-09-01 |
| language | English |
| token length | at least 1024 Pythia tokens after cleaning |
| license class | CC-BY, CC-BY-SA, or CC0 |
The Hugging Face metadata uses license: other because the corpus contains a
mixture of CC-BY, CC-BY-SA, and CC0 rows.
Cleaning
Cleaning was deterministic and designed to remove PMC serialization artifacts without damaging biomedical prose, chemistry, units, or real math notation.
Removed or normalized artifact classes include:
| artifact class | example |
|---|---|
| Pandoc anchors | {#sec1} |
| escaped citation groups | \[[@bib1]\] |
| numeric bracket citations | \[1, 2\] |
| bare citation markers | [@CR40] |
| empty citation parentheses | (), (;), (--) |
| empty superscript citation shells | ^^, ^,^, ^--^ |
| cross-reference links | [Figure 1](#fig1){ref-type="fig"} |
| LaTeX document wrappers | \documentclass, \begin{document} |
| raw HTML/XML tags | <p>, </italic> |
| Word field-code remnants | MERGEFORMAT |
| confirmed escaped literal punctuation | \*, \_, \# |
| markdown image placeholders |  |
| generic markdown links | [label](https://example.org) |
| Pandoc smallcaps spans | [TEXT]{.smallcaps} |
| orphan bracket shells | [[ word, [] |
| dense markdown-table pipes | ` |
Ambiguous doubled backslashes and escaped parentheses are deliberately not auto-stripped because they can be legitimate LaTeX, math, or prose notation.
Truncation
Each selected row is a deterministic prefix of the cleaned parent document. The pipeline uses a three-tier boundary hierarchy:
| boundary type | train | test |
|---|---|---|
| paragraph | 8 | 1 |
| sentence | 9965 | 997 |
| token-boundary cutoff | 27 | 2 |
Processing Summary
| stage | rows |
|---|---|
| rows scanned | 27,000 |
| eligible after filtering | 24,846 |
| unique eligible after deduplication | 24,843 |
| selected train rows | 10,000 |
| selected test rows | 1,000 |
| unused eligible rows | 13,843 |
Date Distribution
| publication year | train | test |
|---|---|---|
| 2020 | 1142 | 109 |
| 2021 | 2307 | 234 |
| 2022 | 2538 | 248 |
| 2023 | 3165 | 323 |
| 2024 | 848 | 86 |
Minimum selected publication date:
2020-09-01
License Distribution
| license class | train | test |
|---|---|---|
| CC-BY | 9962 | 996 |
| CC-BY-SA | 6 | 2 |
| CC0 | 32 | 2 |
Verification
The local review notebook re-scans every exported row. All strict artifact detectors pass with zero affected rows in both train and test:
| strict artifact class | train | test |
|---|---|---|
| residual pandoc anchors | 0 | 0 |
| escaped-bracket citations | 0 | 0 |
| numeric bracket citations | 0 | 0 |
| dash-only citation remnants | 0 | 0 |
| empty citation parentheses | 0 | 0 |
| empty superscript citation shells | 0 | 0 |
| LaTeX document wrappers | 0 | 0 |
| raw HTML/XML tags | 0 | 0 |
| cross-reference links | 0 | 0 |
| bare citation markers | 0 | 0 |
| Word MERGEFORMAT artifacts | 0 | 0 |
| escaped literal punctuation | 0 | 0 |
| markdown image placeholders | 0 | 0 |
| generic markdown links | 0 | 0 |
| Pandoc smallcaps markup | 0 | 0 |
| orphan bracket shells | 0 | 0 |
| dense markdown-table pipes | 0 | 0 |
Ordered sequence hashes over the public text column:
train_text_sequence_sha256 = 3f5767c782aca43da42cce8b456afb1e95e100b73c0abf4d4406e7d3b273338a
test_text_sequence_sha256 = e5207234ecbd3e80a41348a10da42a6c3ad36bba1e3c612e70f3dbbded77d37d
Reproducibility
| field | value |
|---|---|
| preprocessing notebook | pmc_1024_2040_preprocessing.ipynb |
| review notebook | pmc_1024_2040_dataset_review.ipynb |
| artifact repair notebook | pmc_1024_2040_artifact_repair.ipynb |
| preprocessing version | pmc_1024_2040 |
| seed | 42 |
| tokenizer | EleutherAI/pythia-2.8b |
| final audit timestamp | 2026-07-30T21:23:35.624609+00:00 |
Use this corpus only under the token and cleaning contract documented above.
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